#!/bin/bash
cd /mnt/e/HCP35/unzipped/;
# List of folders
folders=("mgh_1001" \
"mgh_1008" \
"mgh_1015" \
"mgh_1022" \
"mgh_1029" \
"mgh_1002" \
"mgh_1009" \
"mgh_1016" \
"mgh_1023" \
"mgh_1030" \
"mgh_1003" \
"mgh_1010" \
"mgh_1017" \
"mgh_1024" \
"mgh_1031" \
"mgh_1004" \
"mgh_1011" \
"mgh_1018" \
"mgh_1025" \
"mgh_1032" \
"mgh_1005" \
"mgh_1012" \
"mgh_1019" \
"mgh_1026" \
"mgh_1033" \
"mgh_1006" \
"mgh_1013" \
"mgh_1027" \
"mgh_1034" \
"mgh_1007" \
"mgh_1014" \
"mgh_1021" \
"mgh_1028")

for folder in "${folders[@]}"; do
#Run the Freesurfer segmentation tool
SUBJECTS_DIR=/mnt/e/HCP35/unzipped/${folder}/anat/T1;
mri_segment_thalamic_nuclei_dti_cnn \
--t1 /mnt/e/HCP35/unzipped/${folder}/anat/T1/T1/mri/norm.mgz \
--aseg /mnt/e/HCP35/unzipped/${folder}/anat/T1/T1/mri/aseg.mgz \
--fa /mnt/e/HCP35/unzipped/${folder}/anat/T1/T1/dmri/dtifit_FA.nii.gz \
--v1 /mnt/e/HCP35/unzipped/${folder}/anat/T1/T1/dmri/dtifit_V1.nii.gz \
--o /mnt/e/HCP35/unzipped/${folder}/anat/T1/thal_cnn_outputSegmentation.nii.gz \
--vol /mnt/e/HCP35/unzipped/${folder}/anat/T1/thal_cnn_volumes_new_model_new_script.csv \
--model /usr/local/freesurfer/7.4.1/models/thalseg_1.1.h5 \
--threads 3
done
